{"action":"created","issue":{"url":"https://api.github.com/repos/ANTsX/ANTsR/issues/192","repository_url":"https://api.github.com/repos/ANTsX/ANTsR","labels_url":"https://api.github.com/repos/ANTsX/ANTsR/issues/192/labels{/name}","comments_url":"https://api.github.com/repos/ANTsX/ANTsR/issues/192/comments","events_url":"https://api.github.com/repos/ANTsX/ANTsR/issues/192/events","html_url":"https://github.com/ANTsX/ANTsR/issues/192","id":270017075,"number":192,"title":"Pandoc error with devtools::check()","user":{"login":"cookpa","id":611507,"avatar_url":"https://avatars2.githubusercontent.com/u/611507?v=4","gravatar_id":"","url":"https://api.github.com/users/cookpa","html_url":"https://github.com/cookpa","followers_url":"https://api.github.com/users/cookpa/followers","following_url":"https://api.github.com/users/cookpa/following{/other_user}","gists_url":"https://api.github.com/users/cookpa/gists{/gist_id}","starred_url":"https://api.github.com/users/cookpa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cookpa/subscriptions","organizations_url":"https://api.github.com/users/cookpa/orgs","repos_url":"https://api.github.com/users/cookpa/repos","events_url":"https://api.github.com/users/cookpa/events{/privacy}","received_events_url":"https://api.github.com/users/cookpa/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-10-31T16:03:06Z","updated_at":"2017-10-31T16:05:32Z","closed_at":null,"author_association":"COLLABORATOR","body":"I'm trying to run devtools::check() on some updated code, and I'm getting this error with the ANTsR.Rmd (which I have not modified). I am running devtools 1.13.3 and pandoc 2.0.0.1.\r\n\r\n\r\ndevtools::check()\r\nUpdating ANTsR documentation\r\nLoading ANTsR\r\nSetting env vars -----------------------------------------------------------------------------------------------------\r\nCFLAGS  : -Wall -pedantic\r\nCXXFLAGS: -Wall -pedantic\r\nBuilding ANTsR -------------------------------------------------------------------------------------------------------\r\n'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD  \\\r\n  build '/Users/pcook/code/ANTsR' --no-resave-data --no-manual \r\n\r\n* checking for file ‘/Users/pcook/code/ANTsR/DESCRIPTION’ ... OK\r\n* preparing ‘ANTsR’:\r\n* checking DESCRIPTION meta-information ... OK\r\n* cleaning src\r\n* running ‘cleanup’\r\n* installing the package to build vignettes\r\n* creating vignettes ... ERROR\r\n--smart/-S has been removed.  Use +smart or -smart extension instead.\r\nFor example: pandoc -f markdown+smart -t markdown-smart.\r\nTry pandoc --help for more information.\r\nError: processing vignette 'ANTsR.Rmd' failed with diagnostics:\r\npandoc document conversion failed with error 2\r\nExecution halted\r\nError: Command failed (1)\r\n"},"comment":{"url":"https://api.github.com/repos/ANTsX/ANTsR/issues/comments/340812068","html_url":"https://github.com/ANTsX/ANTsR/issues/192#issuecomment-340812068","issue_url":"https://api.github.com/repos/ANTsX/ANTsR/issues/192","id":340812068,"user":{"login":"muschellij2","id":1075118,"avatar_url":"https://avatars2.githubusercontent.com/u/1075118?v=4","gravatar_id":"","url":"https://api.github.com/users/muschellij2","html_url":"https://github.com/muschellij2","followers_url":"https://api.github.com/users/muschellij2/followers","following_url":"https://api.github.com/users/muschellij2/following{/other_user}","gists_url":"https://api.github.com/users/muschellij2/gists{/gist_id}","starred_url":"https://api.github.com/users/muschellij2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/muschellij2/subscriptions","organizations_url":"https://api.github.com/users/muschellij2/orgs","repos_url":"https://api.github.com/users/muschellij2/repos","events_url":"https://api.github.com/users/muschellij2/events{/privacy}","received_events_url":"https://api.github.com/users/muschellij2/received_events","type":"User","site_admin":false},"created_at":"2017-10-31T16:05:32Z","updated_at":"2017-10-31T16:05:32Z","author_association":"CONTRIBUTOR","body":"Please see https://github.com/rstudio/rmarkdown/issues/1120\nRecommend solution: install new markdown as pandoc 2 is out:\n\ndevtools::install_github(\"rstudio/rmarkdown\")\n\n\nJohn\n\nOn Tue, Oct 31, 2017 at 12:03 PM, Philip Cook <notifications@github.com>\nwrote:\n\n> I'm trying to run devtools::check() on some updated code, and I'm getting\n> this error with the ANTsR.Rmd (which I have not modified). I am running\n> devtools 1.13.3 and pandoc 2.0.0.1.\n>\n> devtools::check()\n> Updating ANTsR documentation\n> Loading ANTsR\n> Setting env vars ------------------------------\n> -----------------------------------------------------------------------\n> CFLAGS : -Wall -pedantic\n> CXXFLAGS: -Wall -pedantic\n> Building ANTsR ------------------------------\n> -------------------------------------------------------------------------\n> '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file\n> --no-environ --no-save --no-restore --quiet CMD\n> build '/Users/pcook/code/ANTsR' --no-resave-data --no-manual\n>\n>    - checking for file ‘/Users/pcook/code/ANTsR/DESCRIPTION’ ... OK\n>    - preparing ‘ANTsR’:\n>    - checking DESCRIPTION meta-information ... OK\n>    - cleaning src\n>    - running ‘cleanup’\n>    - installing the package to build vignettes\n>    - creating vignettes ... ERROR\n>    --smart/-S has been removed. Use +smart or -smart extension instead.\n>    For example: pandoc -f markdown+smart -t markdown-smart.\n>    Try pandoc --help for more information.\n>    Error: processing vignette 'ANTsR.Rmd' failed with diagnostics:\n>    pandoc document conversion failed with error 2\n>    Execution halted\n>    Error: Command failed (1)\n>\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/ANTsX/ANTsR/issues/192>, or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/ABBnrqfotXhVjddQp0hpeJafcfaoe32Kks5sx0S6gaJpZM4QM_m1>\n> .\n>\n"}}
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